1. STS-111 - "I Got You Babe" from Groundhog Day

On June 19, 2002, the crew of the Space Shuttle Endeavour awoke to a tinny rendition of "I Got You Babe" by Sonny and Cher, taken from the Groundhog Day soundtrack. This song was chosen because the crew, much like Bill Murray's character in Groundhog Day, was caught in a loop, repeating the previous day's deorbit activities, hoping to land that day if weather cooperated. In Groundhog Day, Murray's character was repeatedly awakened by "I Got You Babe" at 6am each morning. NASA's history notes (emphasis added):

For commander Ken Cockrell this was his third mission in a row where he's stayed in orbit for an additional two days in the hopes of good weather in Florida. On STS-80 the landing finally cooperated and he landed in Florida, for STS-98 and STS-111 he landed at the alternate site in California.

You can hear the wakeup (WAV file), including a nod to Groundhog Day at the end.

Although "I Got You Babe" was the last wakeup call for STS-111, its first was "Gettin' Jiggy wit It" by Will Smith. Smith's song was intended for Mission Specialist Valery Korzun, who took command of the International Space Station that day.

2. STS-44 - Patrick Stewart

On November 25, 1991, the crew of Atlantis was treated to an extended wakeup call recorded by Patrick Stewart, who was four years into his star turn as Captain Jean-Luc Picard of the USS Enterprise on Star Trek: The Next Generation. At the TNG theme played, Stewart intoned:

"Space: the final frontier.
This is the voyage of the Space Shuttle Atlantis.
Its ten-day mission:
To explore new methods of remote sensing and observation of the planet Earth...
To seek out new data on radiation in space, and a new understanding of the effects of microgravity on the human body...To boldly go where two hundred and fifty-five men and women have gone before!"

"Hello Fred, Tom, Story, Jim, Tom, and especially Mario -- this is Patrick Stewart, choosing not to outrank you as Captain Jean-Luc Picard, saying that we are confident of a productive and successful mission. Make it so."

Mission Specialist Mario Runco was a Trek fan, you see.

3. STS-26 - Robin Williams

On September 30, 1988, actor Robin Williams woke the crew by announcing, "Good morning, Discovery!" in the style of his 1987 hit movie Good Morning, Vietnam. This was the first wakeup call of the first Shuttle mission after the Challenger disaster in 1986, so a little levity was called for. After that intro, a modified version of the "Green Acres" theme played, with newly recorded Shuttle-appropriate lyrics, followed by two other songs. (Details of the lyrics and the other two songs are not listed in NASA's historical record.)

4. STS-9 - All Work and No Play

The crew of STS-9 worked around the clock in shifts from November 28 through December 8, 1983. Because of this, no wakeup calls were transmitted. (STS-9 was the Shuttle mission carrying the first Spacelab module to orbit; it also contained the largest crew of any space mission to date -- six men.) A similar round-the-clock schedule was maintained on STS-51-F in 1985 and many other missions afterwards.

5. STS-29 - William Shatner

On March 16, 1989, the Discovery crew started their day with the "Star Trek" theme, then comments from William Shatner congratulating the astronauts on their mission. Mission Control then played fight songs from various crew members' alma maters. Finally CAPCOM G. David Low said, "Discovery, [this is] Houston -- beam me up, Scotty!"

Shatner made another wakeup call for STS-133 on March 7, 2011:

6. STS-29 - Kids

I'll just quote NASA's history of wakeup calls directly for this adorable moment from March 18, 1989:

Mission Control sent recordings of astronauts' children shouting such things as "Get up, Dad, get out of bed and get to work" and "Hi, daddy, this is your darling daughter telling you to wake up." This was followed by "What a Wonderful World" by Louis Armstrong. The crew responded with "Homeward Bound" by Simon and Garfunkel.

Discovery landed safely later that day, concluding STS-29. Simon and Garfunkel's "Homeward Bound" has been played five times for returning astronauts.

7. STS-37 - Tom Selleck as "Magnum PI"

On April 11, 1991 the Atlantis crew was greeted by the "Magnum PI" theme song, followed by Tom Selleck greeting Mission Specialist Linda Goodwin: "Good morning, and a special wakeup to Linda. This is Tom Selleck and I hope you had a nice night's sleep, but it's time to get up and go to work." The crew landed safely later that day, and NASA's history notes that Goodwin was "a big Selleck fan."

8. STS-53 - The Singing Dogs

The crew of STS-53 were known unofficially as "Dog Crew I," after dubbing themselves the "Dogs of War," because their flight was supposed to be the last one devoted to Defense Department work. For their first wakeup call of the mission on December 3, 1992, Mission Control played a version of "Jingle Bells" performed by The Singing Dogs, a creation of Dr. Demento. Carl Meade at Mission Control said, "Crew dogs, wake up. We got work to do." Commander David Walker responded, "Good morning, Carl. Dogs of War are wide awake." The next morning the crew was greeted with "I Wanna Be a Dog" by Nancy Cassidy.

Interestingly, there was a Dog Crew II on STS-69. Starting on September 8, 1995 that crew was treated to a series of dog-themed wakeup calls, including "Hound Dog" by Elvis, the "Scooby Doo" theme, "Bingo" (performed by Pilot Kenneth Cockrell's five-year-old daughter's kindergarten class), the "Rin Tin Tin" theme, "A Hard Day's Night" by The Beatles, the "Underdog" theme song, "He's a Tramp" from Lady and the Tramp, and finally "Snoopy's Theme" from Peanuts. In 2001, Cockrell was subjected to "Who Let the Dogs Out" as a tribute to his time on the Dog Crew II. You can hear Cockrell's bemused reaction (WAV file) to the song, following an awkward exchange with Mission Control.

9. STS-107 - "Amazing Grace"

STS-107 was Columbia's last flight; the orbiter broke up upon reentry and all seven crew members were killed, making the string of wakeup calls on their mission extremely poignant. Midway through the mission, on January 19, 2003, "Amazing Grace" was played for Mission Specialist Laurel Clark, who was on her first spaceflight. The same song had been played on bagpipes at her wedding, and was later played at her funeral. On the same morning, Radiohead's "Fake Plastic Trees" was played for Pilot William "Willie" McCool.

Later during the mission, on January 29, 2003, John Lennon's "Imagine" was played for McCool and Payload Specialist Ilan Ramon, the first Israeli astronaut. McCool and Ramon noted that from orbit, no borders on Earth were visible, and that the astronauts hoped the people of Earth could live in peace. Ramon proceeded to translate words from the song in Hebrew. "Imagine" was played at Ramon's funeral, ending with a recording of Ilan's voice from the Shuttle, speaking Lennon's words in Hebrew: "You may say I'm a dreamer, but I'm not the only one." You can hear an MP3 of the song and the astronauts' remarks, though it may make you weep.

10. "Star Wars" Theme

Perhaps the most predictable wakeup song imaginable was the "Star Wars" theme composed by John Williams. Various "Star Wars" music was played eight times for NASA wakeup calls, starting in 1984, then proceeding through missions in 1988, 1993, 1996 (both the main theme and "Darth Vader's Theme"), 1999, 2007, and 2009. That 2009 song (MP3) was actually the "Cantina Band" theme, which the crew referred to as a "loony wakeup song" (I can only hope it's NASA's policy to emphasize that Han shot first).

11. STS-135 - "Good Day Sunshine," "Man on the Moon," "Rocket Man," "Run the World (Girls)"

The last Shuttle mission featured lots of great music, including a special wakeup message from Elton John along with "Rocket Man," a perennial NASA favorite. Beyoncé greeted the crew with "Run the World (Girls)" and a recorded message. Michael Stipe of R.E.M. sang an a cappella version of their hit song "Man on the Moon" and commented, "I recorded 'Man on The Moon' for NASA in Venice, Italy, where Galileo first presented to the Venetian government his eight-power telescope, and in 1610 wrote 'The Starry Messenger' (Sidereus Nuncius), an account of his early astronomical discoveries that altered forever our view of our place in the universe." The capper came on July 15, 2011, when Sir Paul McCartney woke the crew, saying "Good morning guys, wake up! And good luck on this, your last mission. Well done," after The Beatles' song "Good Day Sunshine" played. The last wakeup song for the Shuttle program was Irving Berlin's "God Bless America" performed by Kate Smith, and Mission Control staff stood at attention as it played. Although the Shuttle program has ended, the ISS still receives regular wakeup calls.

Lots More

This list is just scratching the surface of the amazing wakeup call history compiled by NASA Historian Colin Fries. You can read his history (PDF link) for tons more, which also includes links to many of the more modern wakeup call recordings. I should also note that the Beach Boys appear dozens of times, and Wagner's "Ride of the Valkyries" shows up a lot too.